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Resource file path from simulation#1410

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jkumwenda wants to merge 78 commits intomasterUCL/TLOmodel:masterfrom jkumwenda/resource_file_pathUCL/TLOmodel:jkumwenda/resource_file_pathCopy head branch name to clipboard

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Commits on Jul 2, 2024

• #Read function and enhanced lifestyle

  jkumwenda

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Commits on Jul 4, 2024

• Updated the resource file path and register function in simulation.py

  jkumwenda

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• Implemented resourcefilepath for Disease modules to get resource file path from simulation

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Commits on Jul 30, 2024

• RTI and associated modules

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Commits on Jul 31, 2024

• Schisto and associated modules

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Commits on Aug 8, 2024

• analysis_malaria and associated files

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• analysis file of hiv and associated file, fixed test_schisto

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Commits on Aug 9, 2024

• epi analyses and associated files, removed unused import in analysis rti

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• diarhhhoea analyses and associated files, removed unused import in analysis rti_deaths, re-worked test_rti

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Commits on Aug 14, 2024

• analyses_copd_prev and associated files

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Commits on Aug 15, 2024

• alri analyses and associated files, fixed test_enhanced_lifestyle.py

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Commits on Aug 16, 2024

• prostate_cancer_analyses_logging and associated files, fixed test_healthcareseeking

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Commits on Aug 19, 2024

• other_adult_cancers_analyses_logging and associated files, isort prostate cancer, fixed test equipment and dxmanager

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Commits on Aug 20, 2024

• analysis_measles.py measles.py test_measles.py fixed for resource file path from simulation.py.

  jkumwenda

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• analysis_measles_deaths.py fixed for resource file path from simulation.py.

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Commits on Aug 22, 2024

• analysis_measles.py removed unused from pathlib import Path .

  jkumwenda

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• breast_cancer_analyses_logging.py calc_5y_survival_following_treatment.py and breast_cancer.py method updated for resource file path from simulation.py

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• breast_cancer_analyses_logging.py calc_5y_survival_following_treatment.py and breast_cancer.py method updated for resource file path from simulation.py

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• breast_cancer_analyses_logging.py calc_5y_survival_following_treatment.py isort the import to fix incorrectly sorted error

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Commits on Aug 23, 2024

• bladder_cancer_analyses_single_run, calc_5y and associated files, convert to path in simulation

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Commits on Aug 26, 2024

• fix resourcefilepath for test_beddays and test_cons

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• fix test_demography and associated files, fixed fullmodel file

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Commits on Aug 27, 2024

• fix test utils, labour and newborn_outcomes

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Commits on Aug 28, 2024

• fix test_postnatal, pregnancy_supervisor, htm_scaleup, rmv unused import in fullmodel

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Commits on Aug 29, 2024

• fix test healthburden, control_order_of_events, maternal_health_helper_and_analysis_funcs

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• oesophageal cancer survival_following_treatment, analyses_depression_run_me and associated files

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Commits on Aug 30, 2024

• cardiometabolicdisorders_plots(NR) and associated files, test symptommanager and antenatal_interventions

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• tb (NR), stunting (NR) analyses and associated files

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Commits on Sep 2, 2024

• fix tests epi and simplified_births

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• all remaining NR anayses

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Commits on Sep 3, 2024

• fix tests contraception, module_dependencies, fullmodel and determinism via scale_run

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Commits on Sep 4, 2024

• fix tests logging_end_to_end, basic_sims, find_events, breast_cancer

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• fix tests healthsystem, analysis

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Commits on Sep 5, 2024

• Merge branch 'master' into jkumwenda/resource_file_path

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• fix failing tests after merging

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Commits on Sep 27, 2024

• Merge branch 'master' into jkumwenda/resource_file_path

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• to be debugged

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Commits on Sep 30, 2024

• update simulation file

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• Merge remote-tracking branch 'origin/jkumwenda/resource_file_path' into jkumwenda/resource_file_path

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• update the simulation file

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• fix errors in scenario and tes_sim

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Commits on Oct 2, 2024

• update to scenario and tlo_parameters

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Commits on Oct 3, 2024

• fix test_module_dependencies, health_system, simulation

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• fix scripts

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Commits on Oct 4, 2024

• fix hiv_tb_calibration file res access, and test to check resourcefilepath is set

  thewati

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Commits on Oct 5, 2024

• remove unexpected resourcefilepath in simulation

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Commits on Oct 8, 2024

• Merge branch 'master' into jkumwenda/resource_file_path

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Commits on Oct 9, 2024

• review resourcefilepath in sim and rmv spaces in scenario

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Commits on Oct 11, 2024

• Rollback scenario.py

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Commits on Jan 9, 2025

• Merge branch 'master' into jkumwenda/resource_file_path

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Commits on Jan 10, 2025

• Merge branch 'master' into jkumwenda/resource_file_path

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• Fixed the contraception resourcepath in data_parameters()

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• Fixed the contraception resourcepath in data_parameters()

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Commits on Jan 14, 2025

• Merge remote-tracking branch 'origin/jkumwenda/resource_file_path' into jkumwenda/resource_file_path

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• Malaria methods resource file path

  jkumwenda

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• Updated resourcefilepath = './resources' to the resourcefilepath = Path("./resources") in scripts files and updated methods read parameters to def read_parameters(self, resourcefilepath: Optional[P…

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Commits on Jan 15, 2025

• Merge branch 'master' into jkumwenda/resource_file_path

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• update the resource path in contraception.py Path(self.sim.modules['Contraception'].resourcefilepath)

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• update the resource path in contraception.py Path(self.sim.modules['Contraception'].resourcefilepath)

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• upated the HIV Calibration xls["MPHIA_incidence2015"] to 2020 the current activ resource file in the HIV resource folder

  jkumwenda

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• import Path in chronicsyndrome.py

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• fixed resource file path read_parameters call data def read_parameters(self, resourcefilepath: Optional[Path] = None):

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• Imports are correctly sorted and/or formatted.

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• Imports are correctly sorted and/or formatted.

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• Imports are correctly sorted and/or formatted.

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• Imports are correctly sorted and/or formatted.

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• scenario_switcher.py does not require resourcefilepath, remmove if resourcefilepath is None:

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• scenario_switcher.py does not require resourcefilepath, remmove if resourcefilepath is None:

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• scenario_switcher.py does not require resourcefilepath, remmove if resourcefilepath is None:

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• scenario_switcher.py does require resourcefilepath, remmove if resourcefilepath is None:

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Commits on Jan 16, 2025

• scenario_switcher.py does require resourcefilepath, remmove if resourcefilepath is None:

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• Merge remote-tracking branch 'origin/jkumwenda/resource_file_path' into jkumwenda/resource_file_path

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Commits on Jan 21, 2025

• Merge branch 'master' into jkumwenda/resource_file_path

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• scenario_switcher.py resource file path update in read_parameters

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Commits on Jan 27, 2025

• scenario switcher suggestion

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• Merge branch 'master' into jkumwenda/resource_file_path

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Commits on Jan 28, 2025

• fix error after merge

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• convert path and check existence

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